Starting phenix.real_space_refine on Thu Feb 15 02:52:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew0_31343/02_2024/7ew0_31343_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew0_31343/02_2024/7ew0_31343.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew0_31343/02_2024/7ew0_31343.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew0_31343/02_2024/7ew0_31343.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew0_31343/02_2024/7ew0_31343_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ew0_31343/02_2024/7ew0_31343_updated.pdb" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.076 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1983 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 64 5.16 5 C 5734 2.51 5 N 1519 2.21 5 O 1670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 238": "OE1" <-> "OE2" Residue "A GLU 239": "OE1" <-> "OE2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "C GLU 22": "OE1" <-> "OE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "D GLU 141": "OE1" <-> "OE2" Residue "D GLU 249": "OE1" <-> "OE2" Residue "D GLU 317": "OE1" <-> "OE2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E GLU 153": "OE1" <-> "OE2" Residue "E GLU 220": "OE1" <-> "OE2" Residue "E GLU 246": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8987 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1838 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 225} Chain breaks: 1 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "D" Number of atoms: 2280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2280 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 6, 'TRANS': 277} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'JEU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.06, per 1000 atoms: 0.56 Number of scatterers: 8987 At special positions: 0 Unit cell: (96.05, 123.25, 129.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 64 16.00 O 1670 8.00 N 1519 7.00 C 5734 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS D 184 " - pdb=" SG CYS D 191 " distance=2.03 Simple disulfide: pdb=" SG CYS D 282 " - pdb=" SG CYS D 287 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.25 Conformation dependent library (CDL) restraints added in 1.7 seconds 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2138 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 13 sheets defined 33.0% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.60 Creating SS restraints... Processing helix chain 'A' and resid 9 through 31 removed outlier: 3.542A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA A 31 " --> pdb=" O GLY A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 272 through 280 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 309 removed outlier: 3.757A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 350 Processing helix chain 'B' and resid 2 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'C' and resid 8 through 24 removed outlier: 4.136A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 45 through 47 No H-bonds generated for 'chain 'C' and resid 45 through 47' Processing helix chain 'D' and resid 23 through 32 removed outlier: 3.586A pdb=" N ARG D 27 " --> pdb=" O ASP D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 72 Processing helix chain 'D' and resid 79 through 104 removed outlier: 3.994A pdb=" N PHE D 83 " --> pdb=" O PRO D 79 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ILE D 84 " --> pdb=" O MET D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 109 No H-bonds generated for 'chain 'D' and resid 107 through 109' Processing helix chain 'D' and resid 114 through 147 removed outlier: 3.514A pdb=" N LEU D 136 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA D 139 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 180 Proline residue: D 178 - end of helix Processing helix chain 'D' and resid 200 through 235 removed outlier: 3.567A pdb=" N LEU D 212 " --> pdb=" O THR D 208 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N TYR D 225 " --> pdb=" O TYR D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 268 removed outlier: 3.928A pdb=" N SER D 263 " --> pdb=" O ILE D 259 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE D 265 " --> pdb=" O VAL D 261 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE D 266 " --> pdb=" O LEU D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 281 removed outlier: 4.134A pdb=" N VAL D 280 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLY D 281 " --> pdb=" O LEU D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 291 No H-bonds generated for 'chain 'D' and resid 289 through 291' Processing helix chain 'D' and resid 296 through 313 removed outlier: 3.716A pdb=" N ALA D 300 " --> pdb=" O PHE D 296 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER D 304 " --> pdb=" O ALA D 300 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY D 305 " --> pdb=" O VAL D 301 " (cutoff:3.500A) Proline residue: D 308 - end of helix Processing helix chain 'D' and resid 316 through 324 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.934A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ILE A 221 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE A 199 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 81 through 83 removed outlier: 3.605A pdb=" N ALA B 73 " --> pdb=" O ALA B 60 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 111 through 114 removed outlier: 3.641A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 178 through 181 removed outlier: 3.545A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 190 through 192 removed outlier: 3.621A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.774A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N CYS B 250 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 46 through 52 removed outlier: 3.754A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA B 328 " --> pdb=" O GLY B 319 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.779A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.551A pdb=" N SER E 25 " --> pdb=" O GLN E 3 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N VAL E 5 " --> pdb=" O SER E 23 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 93 through 99 removed outlier: 3.879A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR E 50 " --> pdb=" O TYR E 59 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 140 through 142 removed outlier: 3.623A pdb=" N VAL E 155 " --> pdb=" O ILE E 216 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.887A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'E' and resid 225 through 231 removed outlier: 3.600A pdb=" N VAL E 226 " --> pdb=" O GLN E 179 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE E 177 " --> pdb=" O TYR E 228 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 356 hydrogen bonds defined for protein. 1044 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.28 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 1443 1.28 - 1.41: 2324 1.41 - 1.54: 5300 1.54 - 1.68: 10 1.68 - 1.81: 91 Bond restraints: 9168 Sorted by residual: bond pdb=" C22 JEU D 401 " pdb=" O27 JEU D 401 " ideal model delta sigma weight residual 1.322 1.427 -0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" C23 JEU D 401 " pdb=" C25 JEU D 401 " ideal model delta sigma weight residual 1.424 1.526 -0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" C13 JEU D 401 " pdb=" C14 JEU D 401 " ideal model delta sigma weight residual 1.461 1.409 0.052 2.00e-02 2.50e+03 6.73e+00 bond pdb=" C VAL D 132 " pdb=" O VAL D 132 " ideal model delta sigma weight residual 1.237 1.208 0.029 1.17e-02 7.31e+03 6.02e+00 bond pdb=" C ARG E 191 " pdb=" O ARG E 191 " ideal model delta sigma weight residual 1.242 1.217 0.024 1.00e-02 1.00e+04 5.81e+00 ... (remaining 9163 not shown) Histogram of bond angle deviations from ideal: 100.54 - 116.24: 6132 116.24 - 131.95: 6253 131.95 - 147.66: 20 147.66 - 163.36: 0 163.36 - 179.07: 1 Bond angle restraints: 12406 Sorted by residual: angle pdb=" N PHE D 237 " pdb=" CA PHE D 237 " pdb=" C PHE D 237 " ideal model delta sigma weight residual 111.28 120.03 -8.75 1.09e+00 8.42e-01 6.45e+01 angle pdb=" N ILE E 189 " pdb=" CA ILE E 189 " pdb=" C ILE E 189 " ideal model delta sigma weight residual 106.61 118.33 -11.72 1.78e+00 3.16e-01 4.33e+01 angle pdb=" C ILE E 189 " pdb=" CA ILE E 189 " pdb=" CB ILE E 189 " ideal model delta sigma weight residual 111.09 103.88 7.21 1.11e+00 8.12e-01 4.22e+01 angle pdb=" N ARG D 234 " pdb=" CA ARG D 234 " pdb=" C ARG D 234 " ideal model delta sigma weight residual 111.36 117.93 -6.57 1.09e+00 8.42e-01 3.63e+01 angle pdb=" N SER E 193 " pdb=" CA SER E 193 " pdb=" C SER E 193 " ideal model delta sigma weight residual 110.80 122.57 -11.77 2.13e+00 2.20e-01 3.05e+01 ... (remaining 12401 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4905 17.95 - 35.90: 434 35.90 - 53.84: 94 53.84 - 71.79: 11 71.79 - 89.74: 8 Dihedral angle restraints: 5452 sinusoidal: 2138 harmonic: 3314 Sorted by residual: dihedral pdb=" CB CYS D 184 " pdb=" SG CYS D 184 " pdb=" SG CYS D 191 " pdb=" CB CYS D 191 " ideal model delta sinusoidal sigma weight residual -86.00 -126.70 40.70 1 1.00e+01 1.00e-02 2.32e+01 dihedral pdb=" SG CYS D 184 " pdb=" CB CYS D 191 " pdb=" SG CYS D 191 " pdb=" CA CYS D 191 " ideal model delta sinusoidal sigma weight residual -73.00 1.17 -74.17 1 2.00e+01 2.50e-03 1.75e+01 dihedral pdb=" CB CYS D 282 " pdb=" SG CYS D 282 " pdb=" SG CYS D 287 " pdb=" CB CYS D 287 " ideal model delta sinusoidal sigma weight residual 93.00 125.95 -32.95 1 1.00e+01 1.00e-02 1.54e+01 ... (remaining 5449 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1299 0.072 - 0.144: 110 0.144 - 0.217: 6 0.217 - 0.289: 3 0.289 - 0.361: 2 Chirality restraints: 1420 Sorted by residual: chirality pdb=" CA PHE D 237 " pdb=" N PHE D 237 " pdb=" C PHE D 237 " pdb=" CB PHE D 237 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" CA TYR E 190 " pdb=" N TYR E 190 " pdb=" C TYR E 190 " pdb=" CB TYR E 190 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CA PHE D 133 " pdb=" N PHE D 133 " pdb=" C PHE D 133 " pdb=" CB PHE D 133 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 1417 not shown) Planarity restraints: 1550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 235 " -0.012 2.00e-02 2.50e+03 2.50e-02 6.27e+00 pdb=" C LEU D 235 " 0.043 2.00e-02 2.50e+03 pdb=" O LEU D 235 " -0.016 2.00e-02 2.50e+03 pdb=" N THR D 236 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 131 " 0.011 2.00e-02 2.50e+03 2.14e-02 4.59e+00 pdb=" C SER D 131 " -0.037 2.00e-02 2.50e+03 pdb=" O SER D 131 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL D 132 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR E 235 " 0.035 5.00e-02 4.00e+02 5.24e-02 4.40e+00 pdb=" N PRO E 236 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO E 236 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 236 " 0.030 5.00e-02 4.00e+02 ... (remaining 1547 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 117 2.65 - 3.21: 7957 3.21 - 3.77: 13090 3.77 - 4.34: 16988 4.34 - 4.90: 28854 Nonbonded interactions: 67006 Sorted by model distance: nonbonded pdb=" O SER D 232 " pdb=" CG2 THR D 236 " model vdw 2.087 3.460 nonbonded pdb=" OG SER E 17 " pdb=" O MET E 83 " model vdw 2.249 2.440 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.266 2.440 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.266 2.440 nonbonded pdb=" N ASN E 194 " pdb=" OD1 ASN E 194 " model vdw 2.288 2.520 ... (remaining 67001 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 3.960 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 26.380 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 9168 Z= 0.211 Angle : 0.632 11.771 12406 Z= 0.379 Chirality : 0.044 0.361 1420 Planarity : 0.003 0.052 1550 Dihedral : 14.139 89.739 3305 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.71 % Allowed : 6.10 % Favored : 93.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.22), residues: 1124 helix: 0.24 (0.25), residues: 366 sheet: -0.73 (0.31), residues: 271 loop : -2.04 (0.23), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 176 HIS 0.004 0.000 HIS E 35 PHE 0.010 0.001 PHE D 273 TYR 0.015 0.001 TYR A 230 ARG 0.003 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 165 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: A 306 GLN cc_start: 0.7511 (mm110) cc_final: 0.6969 (tp40) REVERT: D 58 PHE cc_start: 0.7165 (t80) cc_final: 0.6132 (t80) REVERT: D 141 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7189 (tm-30) REVERT: D 183 ASN cc_start: 0.7838 (t0) cc_final: 0.7586 (t0) REVERT: E 47 TRP cc_start: 0.7802 (t60) cc_final: 0.7602 (t60) outliers start: 7 outliers final: 3 residues processed: 170 average time/residue: 0.2098 time to fit residues: 48.6303 Evaluate side-chains 127 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 124 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 194 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 45 optimal weight: 0.7980 chunk 87 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 65 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN B 142 HIS D 63 ASN D 303 ASN E 13 GLN E 232 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.1593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9168 Z= 0.281 Angle : 0.590 10.442 12406 Z= 0.304 Chirality : 0.043 0.181 1420 Planarity : 0.004 0.044 1550 Dihedral : 4.146 49.057 1258 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.85 % Allowed : 15.26 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.24), residues: 1124 helix: 1.24 (0.27), residues: 371 sheet: -0.67 (0.31), residues: 271 loop : -1.74 (0.25), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 176 HIS 0.006 0.001 HIS E 35 PHE 0.022 0.002 PHE D 58 TYR 0.015 0.002 TYR E 235 ARG 0.007 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 124 time to evaluate : 0.984 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7800 (tm-30) cc_final: 0.7524 (tt0) REVERT: A 52 GLN cc_start: 0.7091 (tt0) cc_final: 0.6864 (tt0) REVERT: A 240 MET cc_start: 0.7103 (tmm) cc_final: 0.6896 (tmm) REVERT: A 261 ASP cc_start: 0.8034 (t0) cc_final: 0.7814 (t0) REVERT: D 140 ILE cc_start: 0.7267 (OUTLIER) cc_final: 0.7024 (tt) REVERT: D 141 GLU cc_start: 0.7964 (tm-30) cc_final: 0.7474 (tm-30) REVERT: D 183 ASN cc_start: 0.7928 (t0) cc_final: 0.7602 (t0) REVERT: D 299 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6686 (pp) REVERT: E 76 LYS cc_start: 0.7942 (mtmm) cc_final: 0.7719 (mtmm) REVERT: E 93 MET cc_start: 0.7516 (mpp) cc_final: 0.7095 (mmt) REVERT: E 177 PHE cc_start: 0.5904 (OUTLIER) cc_final: 0.5228 (p90) outliers start: 28 outliers final: 17 residues processed: 144 average time/residue: 0.2064 time to fit residues: 40.9928 Evaluate side-chains 134 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 114 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain E residue 238 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 81 optimal weight: 0.3980 chunk 100 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9168 Z= 0.174 Angle : 0.513 8.697 12406 Z= 0.264 Chirality : 0.040 0.175 1420 Planarity : 0.003 0.039 1550 Dihedral : 3.925 46.817 1257 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.14 % Allowed : 17.90 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.25), residues: 1124 helix: 1.62 (0.28), residues: 366 sheet: -0.52 (0.31), residues: 273 loop : -1.56 (0.25), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 47 HIS 0.004 0.001 HIS E 35 PHE 0.013 0.001 PHE E 203 TYR 0.027 0.001 TYR E 235 ARG 0.004 0.000 ARG D 234 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 124 time to evaluate : 0.925 Fit side-chains REVERT: A 28 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7535 (tt0) REVERT: A 261 ASP cc_start: 0.8033 (t0) cc_final: 0.7827 (t0) REVERT: A 302 TYR cc_start: 0.7969 (t80) cc_final: 0.7750 (t80) REVERT: B 214 ARG cc_start: 0.8094 (mpt180) cc_final: 0.7856 (mpt180) REVERT: D 183 ASN cc_start: 0.7871 (t0) cc_final: 0.7477 (t0) REVERT: E 47 TRP cc_start: 0.7774 (t60) cc_final: 0.7557 (t60) REVERT: E 76 LYS cc_start: 0.7984 (mtmm) cc_final: 0.7636 (mtmm) REVERT: E 93 MET cc_start: 0.7411 (mpp) cc_final: 0.7008 (mmt) REVERT: E 177 PHE cc_start: 0.5802 (OUTLIER) cc_final: 0.5060 (p90) outliers start: 21 outliers final: 12 residues processed: 138 average time/residue: 0.1840 time to fit residues: 35.8500 Evaluate side-chains 126 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 113 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 119 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 243 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 68 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 53 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9168 Z= 0.162 Angle : 0.508 8.866 12406 Z= 0.260 Chirality : 0.040 0.174 1420 Planarity : 0.003 0.046 1550 Dihedral : 3.758 44.074 1255 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.05 % Allowed : 19.23 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.25), residues: 1124 helix: 1.83 (0.28), residues: 366 sheet: -0.41 (0.32), residues: 268 loop : -1.51 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 PHE 0.012 0.001 PHE B 241 TYR 0.027 0.001 TYR E 235 ARG 0.004 0.000 ARG D 234 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 120 time to evaluate : 0.934 Fit side-chains REVERT: A 28 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7525 (tt0) REVERT: A 261 ASP cc_start: 0.8098 (t0) cc_final: 0.7882 (t0) REVERT: A 302 TYR cc_start: 0.7988 (t80) cc_final: 0.7783 (t80) REVERT: B 197 ARG cc_start: 0.7853 (tpp80) cc_final: 0.7341 (tpp80) REVERT: D 67 LEU cc_start: 0.6497 (OUTLIER) cc_final: 0.6271 (mm) REVERT: D 183 ASN cc_start: 0.7786 (t0) cc_final: 0.7346 (t0) REVERT: D 299 LEU cc_start: 0.6999 (OUTLIER) cc_final: 0.6659 (pp) REVERT: E 47 TRP cc_start: 0.7758 (t60) cc_final: 0.7556 (t60) REVERT: E 76 LYS cc_start: 0.7989 (mtmm) cc_final: 0.7627 (mtmm) REVERT: E 93 MET cc_start: 0.7409 (mpp) cc_final: 0.7012 (mmt) REVERT: E 177 PHE cc_start: 0.5833 (OUTLIER) cc_final: 0.5000 (p90) outliers start: 30 outliers final: 19 residues processed: 144 average time/residue: 0.1992 time to fit residues: 40.2230 Evaluate side-chains 136 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 114 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 80 MET Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 177 PHE Chi-restraints excluded: chain E residue 243 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 55 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 294 ASN B 239 ASN ** E 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9168 Z= 0.230 Angle : 0.549 11.838 12406 Z= 0.283 Chirality : 0.041 0.179 1420 Planarity : 0.003 0.052 1550 Dihedral : 3.745 26.359 1253 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 5.19 % Allowed : 19.33 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.25), residues: 1124 helix: 1.79 (0.28), residues: 368 sheet: -0.54 (0.32), residues: 268 loop : -1.55 (0.25), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 47 HIS 0.005 0.001 HIS E 35 PHE 0.017 0.002 PHE B 241 TYR 0.022 0.001 TYR E 235 ARG 0.003 0.000 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 124 time to evaluate : 1.115 Fit side-chains REVERT: A 28 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7608 (tt0) REVERT: A 261 ASP cc_start: 0.8112 (t0) cc_final: 0.7897 (t0) REVERT: A 302 TYR cc_start: 0.8220 (t80) cc_final: 0.8007 (t80) REVERT: B 197 ARG cc_start: 0.7878 (tpp80) cc_final: 0.7388 (tpp80) REVERT: D 67 LEU cc_start: 0.6580 (OUTLIER) cc_final: 0.6140 (mm) REVERT: D 140 ILE cc_start: 0.7232 (OUTLIER) cc_final: 0.6996 (tt) REVERT: D 141 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7563 (tm-30) REVERT: D 183 ASN cc_start: 0.7777 (t0) cc_final: 0.7325 (t0) REVERT: D 299 LEU cc_start: 0.7054 (OUTLIER) cc_final: 0.6737 (pp) REVERT: E 76 LYS cc_start: 0.8031 (mtmm) cc_final: 0.7651 (mtmm) REVERT: E 93 MET cc_start: 0.7518 (mpp) cc_final: 0.7126 (mmt) outliers start: 51 outliers final: 33 residues processed: 161 average time/residue: 0.1854 time to fit residues: 41.3406 Evaluate side-chains 152 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 116 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 228 SER Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 57 CYS Chi-restraints excluded: chain D residue 67 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 140 ILE Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 279 ASP Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain E residue 238 THR Chi-restraints excluded: chain E residue 243 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 9.9990 chunk 21 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 89 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 35 optimal weight: 0.0770 chunk 56 optimal weight: 0.6980 chunk 104 optimal weight: 0.7980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 ASN B 239 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9168 Z= 0.142 Angle : 0.499 10.367 12406 Z= 0.253 Chirality : 0.039 0.143 1420 Planarity : 0.003 0.054 1550 Dihedral : 3.514 23.297 1253 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.26 % Allowed : 21.67 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.25), residues: 1124 helix: 1.98 (0.28), residues: 366 sheet: -0.40 (0.32), residues: 267 loop : -1.43 (0.25), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 47 HIS 0.003 0.000 HIS E 35 PHE 0.011 0.001 PHE D 58 TYR 0.012 0.001 TYR E 235 ARG 0.005 0.000 ARG D 234 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 120 time to evaluate : 0.732 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7561 (tt0) REVERT: A 261 ASP cc_start: 0.8093 (t0) cc_final: 0.7882 (t0) REVERT: B 197 ARG cc_start: 0.7917 (tpp80) cc_final: 0.7426 (tpp80) REVERT: D 141 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7506 (tm-30) REVERT: D 183 ASN cc_start: 0.7702 (t0) cc_final: 0.7255 (t0) REVERT: D 299 LEU cc_start: 0.7175 (OUTLIER) cc_final: 0.6905 (pp) REVERT: E 47 TRP cc_start: 0.7795 (t60) cc_final: 0.7549 (t60) REVERT: E 93 MET cc_start: 0.7473 (mpp) cc_final: 0.7066 (mmt) REVERT: E 177 PHE cc_start: 0.5814 (OUTLIER) cc_final: 0.5093 (p90) outliers start: 32 outliers final: 24 residues processed: 146 average time/residue: 0.1607 time to fit residues: 32.7253 Evaluate side-chains 142 residues out of total 984 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 116 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 258 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 57 CYS Chi-restraints excluded: chain D residue 167 CYS Chi-restraints excluded: chain D residue 172 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 236 THR Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 22 CYS Chi-restraints excluded: chain E residue 45 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 177 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 65 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 43 optimal weight: 0.1980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: